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Try alternative strategy for extracting tags #4928

Merged
merged 88 commits into from
May 1, 2024
Merged

Try alternative strategy for extracting tags #4928

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efe8588
Try alternative strategy for extracting tags
adamrtalbot Feb 15, 2024
ef0eaf0
Add check to prevent confirm pass if no tags present
adamrtalbot Feb 15, 2024
5a184d5
Fix some names for GHA steps
adamrtalbot Feb 15, 2024
692690f
Add fake change in fastp module
adamrtalbot Feb 15, 2024
7cac598
Add fake change in bam_sort_stats_samtools module
adamrtalbot Feb 15, 2024
54750f2
Add fake changes to pytest module and subworkflow
adamrtalbot Feb 15, 2024
b9b1834
Add debug step
adamrtalbot Feb 15, 2024
d588526
fixup
adamrtalbot Feb 15, 2024
73ce73a
Got some variable names wrong...
adamrtalbot Feb 15, 2024
37fb559
Add subworkflows back to nf-tests
adamrtalbot Feb 15, 2024
cc88375
revert confirm-pass if statement
adamrtalbot Feb 15, 2024
0908cad
use JQ to separate modules and subworkflows
adamrtalbot Feb 15, 2024
ae0e2e3
Fix quoting when parsing tags
adamrtalbot Feb 15, 2024
b06e4d2
coerce modules and subworkflows to lower case
adamrtalbot Feb 15, 2024
24c981c
Add specific linting checks to dependencies
adamrtalbot Feb 15, 2024
39ff1ce
Single vs double quotes again
adamrtalbot Feb 15, 2024
8b3d6b7
Some more variable fixing
adamrtalbot Feb 15, 2024
9e9b5cb
this might work
adamrtalbot Apr 5, 2024
065b312
Merge branch 'master' into new_tag_strategy
adamrtalbot Apr 5, 2024
2ddab9a
fixup
adamrtalbot Apr 5, 2024
4dd114a
yet another fixup
adamrtalbot Apr 5, 2024
bc20f2a
Correct modules -> subworkflows
adamrtalbot Apr 5, 2024
2819c54
Fake change to pytest module
adamrtalbot Apr 5, 2024
dc297b8
Correct dependency
adamrtalbot Apr 5, 2024
21cccaa
One more time
adamrtalbot Apr 5, 2024
57fa3b0
More sorting stuff out
adamrtalbot Apr 5, 2024
64c072b
Update modules/nf-core/gunzip/tests/main.nf.test
adamrtalbot Apr 5, 2024
073ae2b
Add fake change to module without nf-test so pytest ONLY is triggered
adamrtalbot Apr 5, 2024
c345358
Merge branch 'master' into new_tag_strategy
adamrtalbot Apr 5, 2024
b606403
Merge branch 'master' into new_tag_strategy
adamrtalbot Apr 9, 2024
acc5b39
fixup incorrect variable
adamrtalbot Apr 10, 2024
7eeb5da
Merge branch 'master' into new_tag_strategy
adamrtalbot Apr 10, 2024
c2ceb2d
Switch to using self-hosted Docker profile
adamrtalbot Apr 10, 2024
c2f09a8
Add dependency checker from Carson Miller
adamrtalbot Apr 11, 2024
6979760
fixup
adamrtalbot Apr 11, 2024
dfcff56
fix(.github/python/find_changed_files.py): detect nf files less greed…
adamrtalbot Apr 11, 2024
703631c
Revert to directories instead of files for module tagging
adamrtalbot Apr 11, 2024
b99e46a
Create optional returntype for Python script
adamrtalbot Apr 11, 2024
a888a91
Remove superfluous python cache
adamrtalbot Apr 11, 2024
c6a06fd
Merge branch 'master' into new_tag_strategy
adamrtalbot Apr 11, 2024
82b40d2
feat: replace custom python with reusable github action for detecting…
adamrtalbot Apr 15, 2024
5d902b5
Fix variable name in output paths
adamrtalbot Apr 15, 2024
2238fe6
Switch to new parents dir syntax
adamrtalbot Apr 15, 2024
2b94d38
prod to bump version of action
adamrtalbot Apr 15, 2024
aeca735
Merge branch 'master' into new_tag_strategy
adamrtalbot Apr 15, 2024
6846f96
Merge branch 'master' into new_tag_strategy
adamrtalbot Apr 16, 2024
3fed071
Merge branch 'master' into new_tag_strategy
adamrtalbot Apr 23, 2024
5a28a91
Update .github/workflows/test.yml
adamrtalbot Apr 23, 2024
173c667
Update .github/workflows/test.yml
adamrtalbot Apr 23, 2024
fc43815
Exclude more subworkflows from Conda
adamrtalbot Apr 23, 2024
9db4b22
Update .github/workflows/test.yml
adamrtalbot Apr 24, 2024
979fe8b
Update .github/workflows/test.yml
adamrtalbot Apr 24, 2024
cde646a
QUILT nf-test and bamlist (#5515)
LouisLeNezet Apr 23, 2024
62f3409
New module: gnu/split (#5428)
k1sauce Apr 24, 2024
a84c33e
Add Demuxem (#5504)
mari-ga Apr 24, 2024
d50427d
Fix AMRFinderPlus (#5521)
jasmezz Apr 24, 2024
951a2dd
fix stubs salmon (#5517)
Lucpen Apr 24, 2024
ab707a2
Update mcquant: Added nf-test and meta.yml information (#5507)
FloWuenne Apr 24, 2024
0b10545
Added repeatmodeler/builddatabase (#5416)
GallVp Apr 25, 2024
891aae4
bump wisecondorx to v1.2.7 (#5523)
nvnieuwk Apr 25, 2024
1f8a032
Add Freemuxlet to modules (#5520)
wxicu Apr 25, 2024
f18f965
chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.4…
renovate[bot] Apr 26, 2024
b2b2180
Updating sentieon to 202308.02 (#5525)
asp8200 Apr 26, 2024
c804f96
Fix stale action (#5530)
edmundmiller Apr 26, 2024
8ffdbb0
Changed tag from single quotes to double quotes (#5531)
LeonHafner Apr 26, 2024
880bd94
[TYPO] Align commas (#5380)
lrauschning Apr 27, 2024
1023de4
GFFREAD: updated to 0.12.7, added meta and fasta input/output (#5448)
GallVp Apr 29, 2024
896d83f
re delete gatk4/bedtointervallist from pytest_modules.yml after it wa…
vlebars Apr 29, 2024
cb2fed3
Update mosdepth to 0.3.8 (#5538)
asp8200 Apr 29, 2024
912e7fd
migrating flash to nf-test (#5470)
DavideBag Apr 29, 2024
f3fb8b7
add riboseq transcriptome bam to test config (#5537)
iraiosub Apr 29, 2024
7a22dfc
Update nanoplot/main.nf (#5460)
ashotmarg Apr 29, 2024
0c817a3
Added repeatmodeler/repeatmodeler (#5536)
GallVp Apr 30, 2024
4441c29
Blastdbcmd new module (#5482)
toniher Apr 30, 2024
7644668
Merge branch 'master' into new_tag_strategy
adamrtalbot Apr 30, 2024
17210f3
Remove fake changes
adamrtalbot Apr 30, 2024
9635f63
Use merge group base ref instead of PR base_ref when merging
adamrtalbot May 1, 2024
a6369df
fixup
adamrtalbot May 1, 2024
0f052bc
Use SHA instead of head ref
adamrtalbot May 1, 2024
2ec307f
fixup
adamrtalbot May 1, 2024
8e6cf9d
work
adamrtalbot May 1, 2024
3408db5
origin/
adamrtalbot May 1, 2024
f7273f8
cmon
adamrtalbot May 1, 2024
c9eb127
one more time with feeling
adamrtalbot May 1, 2024
454616a
fixup again
adamrtalbot May 1, 2024
65047b4
Worth a try
adamrtalbot May 1, 2024
7ef86b9
Increase fetch depth to 2
adamrtalbot May 1, 2024
06bf16b
Use SHA instead of head ref
adamrtalbot May 1, 2024
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